How To Fix Common Seedling Problems

Seedling problems are super frustrating, and many times you’re left wondering “Why do my seedlings keep dying?”. Don’t worry, I’ve got the solutions to your seed starting problems! In this post, I’ll give you detailed fixes and tons of help with seedlings, so you can finally stop struggling.

Help! Why are my seedlings dying? This is one of the most common questions I get from gardeners when they’re starting seeds indoors. If this sounds familiar, and you need help with seedlings, then you’ve come to the right place.

This detailed troubleshooting guide will help you figure out why your seedlings are struggling (or worse, falling over and dying), and give you tons of tips for how to fix common seed starting problems.

Healthy seedlings growing indoors

The Most Common Seed Starting Problems

If you’re struggling with growing seeds indoors, you’re not alone. We have all been there, and everyone who has ever started seeds indoors has had seedling problems at some point (even the seasoned experts!). Don’t worry, many of these issues are easily fixable with a few minor adjustments.

In the troubleshooting sections below, I’ll go into details about the causes and solutions, and I’ll give you tons of help with seedlings. Here’s a list of the most common seedling problems we’ll talk about. You can click the links to skip ahead, or simply keep reading…

Seedling Problems, Causes & Solutions

The good news is that most of these common seedling problems are easily fixable, but you will need to take action pretty quickly to save your seedlings.

So now let’s dig into the help with seedlings part. Below I will walk you through each of the problems listed above, identifying the main causes, and their solutions.

1. Seedlings Falling Over And Dying After Sprouting

Probably the biggest frustration for gardeners is when their seedlings tip over at the base and die without warning. This is called damping off, and is caused by bacterial seedling blight. Damping off is the most common cause of seedlings dying after sprouting.

Unfortunately, damping off happens so fast that there’s really no way to save them once they flop over. The best way to stop it is to prevent it from happening in the first place. Here are the common causes of seedling damping off, and their solutions.

Why are my seedlings falling over and dying (and how to fix it)?

Using the wrong type of soil – Solution: Always use a quality seed starting medium or peat pellets for growing seeds. Don’t use regular potting soil or garden soil. And never, never reuse any of your soil or pellets.

Not enough ventilation – Solution: Remove the plastic dome lids once the seeds have germinated. Keep an oscillating fan blowing over the seedlings to ensure proper ventilation.

Soil kept too wet – Solution: Don’t water your seedlings if the soil is already wet or soggy. Don’t allow the containers to sit in water for extended periods of time. Use a soil moisture gauge so you know when to water.

Watering from the top – Solution: It’s best to water your seedlings from the bottom by pouring water into the tray, and allowing the soil to absorb the water from the bottom. Empty any water that hasn’t been soaked up after 30 minutes.

Reusing dirty trays can cause major seed starting problems

2. Seedlings Turning Yellow, Brown, Or Have Faded Leaves

When seedlings leaves turn brown, yellow, white, or look dull and faded, that’s a sure sign that something is wrong. Most of the time, you can save them but you have to act fast in order for them to survive.

Once you notice that seedling leaves have started to fade or change color, it’s important to figure out what’s wrong and fix it quickly. Many times you can save them, but if the damage is severe, some seedlings may not recover.

These are the most common causes of discolored or faded leaves, and the solutions for how to save your seedlings…

Overwatered seedling – Solution: Make sure the soil is never saturated or soggy, and drain excess water from the trays. A soil water gauge is a great tool to help you give them the perfect amount of moisture.

Fertilizer burn – Solution: Chemical fertilizers are notorious for burning delicate seedlings. Switch to a natural, organic seedling fertilizer rather than using chemical fertilizers. And always be sure to follow instructions on the package.

Sunburn – Solution: Move your seedlings out of the sun immediately (severe sunburn is usually fatal to seedlings). Always be sure to harden off your seedlings properly before moving them outdoors or into direct sunlight.

Wrong type of soil – Solution: If you use the wrong soil for starting seeds, they may not be getting the nutrients they need. Always use a quality seedling soil mix for planting seeds indoors.

Using quality soil helps prevent common seedling problems

3. Weak, Leggy Seedlings

If seedlings don’t get enough light, they will reach and stretch for the brightest light source that’s nearby (usually a window). This is definitely one of the biggest problems with seedlings growing indoors, and also one of the easiest to fix.

However, if you don’t fix the issue that’s causing seedling stems to grow tall and leggy, it won’t take long before they are too weak to recover. If your seedlings have grown so tall that they are falling over… then it’s probably too late to save them.

Seedlings aren’t getting enough light –Solution: Add a grow light, position it so it sits 2-4 inches above the seedlings at all times, and keep it on for 12-14 hours per day. You can buy a grow light system to make this super easy, or make your own grow lights for seedlings using a fluorescent light fixture and plant grow bulbs. It’s also helpful to use an inexpensive outlet timer so you can set it and forget it.

Seedlings are overcrowded and competing for light –Solution: Thin your seedlings by cutting out the weakest ones at the soil level so there’s only one growing per cell or pellet (never pull them out of the soil though). If they have outgrown the small seed cells, then it’s time to transplant them up into seedling pots.

Fix leggy seedlings by putting them under lights

4. Mold Growth In Seed Trays

Mold usually grows on top of the soil, but it could grow on seedlings too. The mold isn’t directly what causes them to die, it’s a symptom of other more severe seedling problems. And if those issues aren’t fixed, your seedlings probably won’t survive for long.

It’s not the mold growing in your trays that will kill your seedlings… it’s the problem(s) causing the mold that you have to be worried about. Once you fix the problem(s), the mold will die.

Overwatered seedling – Solution: Make sure the soil is never soggy or kept constantly wet, and try to allow the very top layer of the soil to dry out a bit between waterings. Water seedlings from the bottom rather than the top. Use a soil moisture meter so you always know when it’s time to water.

Overcrowded seedlings – Solution: Thin out your seedlings so there’s only one growing per cell or pellet. Otherwise, pot them up if they have outgrown their seed tray.

Not enough air circulation – Solution: Add an oscillating fan and position it to blow over your seedlings to give them plenty of airflow, and help to dry out soggy soil.

A fan blowing on seedlings helps prevent problems

5. Tiny Bugs Flying Around Seedlings

Fungus gnats (aka soil gnats) are small bugs that lay their eggs in soil, and they are a common pest indoors. You’ll see them flying around the seedlings, or crawling in the soil.

They’re normally just a nuisance, and won’t damage or kill seedlings if kept under control. Seeing a few gnats flying around is usually not a big deal.

But they are a sign of a bigger problem. So if the infestation is severe, then you need to take quick action to save your seedlings. There is one main thing that causes fungus gnats to infest your seedling trays…

Why are there bugs flying around my seedlings (and how to get rid of them)?

Soil is too wet – Solution: Water seedlings from the bottom so the top of the soil can dry out a bit between waterings. Potting them up will make it easier to control the soil moisture level, and get rid of the fungus gnats. Hang yellow sticky traps near your seedlings to help control the adult gnats. Store all unused soil in an air-tight container.

Use yellow sticky traps to control bug problems with seedlings

6. Seedlings Not Growing, Or Growing Slowly

Sometimes seedlings can grow very, very slowly, or they seem to stop growing all together. Keep in mind that some types of seedlings grow much faster than others do, and that is perfectly normal.

Fast-growing seedlings can get true leaves within a week after germination, while others won’t grow them for several weeks. So if it’s just that your seedlings are not growing true leaves yet, give it more time. However, there are a few problems that can slow or stunt growth…

Why are my seedlings growing so slow (and how to fix it)?

Room temperature is too cold – Solution: Seedling growth can be stunted when it’s too cold in your home. If the room temperature is below 65F degrees, then try keeping seedlings warm using a room space heater or a heat mat.

Not enough light – Solution: Inadequate lighting is another thing that can slow seedling growth. It’s best to always grow seedlings indoors under grow lights, rather than trying to grow them in a sunny window.

Lack of nutrients – Solution: Nutrition is very important for growing seedlings. Once they grow their first true leaves, then start feeding them with organic fertilizer. I recommend using an organic seedling fertilizer, liquid compost tea, or fish emulsion.

Inadequate watering – Solution: Over or under watering can also cause seedlings to grow slower. So keeping the soil evenly moist at all times is super important. I recommend getting a moisture gauge, and checking the soil regularly so you know exactly when to water.

7. Seedling Leaves Curling Up, Down, Or Drooping

Droopy seedlings and curling leaves are both indications that something is definitely wrong, and should be fixed ASAP. Under watering, spider mites, or fertilizer burn are the three main culprits – all of which can quickly kill seedlings.

As soon as you notice the leaves are sagging or curling, take a closer look. If you see webbing on the leaves, between the leaf joints, or tiny bugs on the leaves then it’s probably spider mites.

Here are causes of droopy seedlings or curling leaves, and their solutions…

Why are my seedling leaves curling or drooping (and how to save them)?

Under watering – Solution: Never allow the soil to dry out completely. Consistent under watering can weaken or kill seedlings. Water your dried out seedlings immediately. Severely dehydrated seedlings may not recover.

Spider mites – Solution: Spider mites can kill seedlings very quickly, so it’s important to act fast! Increase the humidity level around your seedlings by misting them or putting them into an indoor greenhouse. You can also use neem oil or insecticidal soap to help get rid of bugs on seedlings (be sure to test it on one seedling first before spraying them all).

Tips For Growing Strong, Healthy Seedlings

The best advice I can offer you to help with seedlings is to try your best to prevent problems from happening in the first place. Many of these are fixable, but some seedlings can’t be saved and you’ll have to start all over from scratch (ugh!).

The good news is that it’s not difficult to care for seedlings, and there are only a few key things to remember. Here are a few quick tips for you…

Don’t feel bad if you’ve experienced any (or all) of these seedling problems, we’ve all been there. It’s best to avoid them all together, and prevention is the most important step you can take.

Once you get the hang of it, you’ll be able to grow healthy seedlings indoors without any problems at all. But of course, if you need more help with seedlings, I’m always here for you!

If you’re tired of struggling to grow your own seeds, then my Starting Seeds Indoors eBook is for you! It’s a quick start guide that will have you planting seeds in no time.

Otherwise, if you want to learn how to grow any plant you want from seed, then enroll in my Seed Starting Course. It’s a wonderful, fun course that will teach you everything you need to know in order to easily grow your own seedlings.

About Amy Andrychowicz

I live and garden in Minneapolis, MN (zone 4b). My green thumb comes from my parents, and I've been gardening most of my life. I’m a passionate gardener who loves growing everything from vegetables, herbs, and flowers to succulents, tropicals, and houseplants - you name, I've grown it! Read More...